Main
Brian M. Schilder 
Passionately pursuing multi-disciplinary research to improve human lives.
Imperial College London
PhD Candidate
ScB, MPhil
Education
Imperial College London
PhD: Clinical Medical Research; Computational Neurogenomics
2024
Supervisors: Nathan G. Skene, PhD; Paul M. Matthews, PhD
Thesis: Multi-omic medicine: dissecting the cell-type-specific and pleiotropic mechanisms underlying disease genomics at scale
- Aim 1) Dissect the multi-scale mechanisms (e.g. genes, pathways, cell-types, phenotypes) underlying Mendelian and complex disease genomics.
- Aim 2) Decompose multi-trait disease genomics and identify the multi-scale mechanisms underlying each latent component.
- Aim 3) Demonstrate reproducibility and make reproducible best practices accessible to others.
The George Washington University
MPhil: Human Paleobiology; Evolutionary Neuroscience & Genomics
2017
Supervisors: Chet C. Sherwood, PhD; Brenda J. Bradley, PhD
Thesis: The evolution of the hippocampus and adult neurogenesis: Novel insights into the origins of human memory
- Aim 1): Identify human-specific features of hippocampal subfield organization, adult neurogenesis, and their ecological correlates.
- Aim 2) Identify human-specific patterns of hippocampal subfield gene expression.
- Aim 3) Identify the genetic mechanisms mediating the evolution of human hippocampal neuroanatomy and gene expression.
Brown University
ScB: Cognitive Neuroscience; Neurological Diseases & Disorders
2011
Supervisors: Sheila E. Blumstein, PhD; David L. Sheinberg, PhD
Core Skills
Research
14+ years of highly multidisciplinary research experience. Creative and rapid hypothesis generation, project design, and problem solving.
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- Fields: Including but not limited to: Neuroscience, systems biology, bioinformatics, machine learning, multi-omics, biomedicine, rare diseases, complex diseases, cognition, statistics, computer science, phylogenetics, paleoanthropology biomechanics, primatology, histology/microscropy.
- Publications: Strong writing skills as evidenced by 22 peer-reviewed scientific publications, 23 international conference posters and 13 successful grant applications.
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Programming
Extensive experience in developing highly reproducible scripts and software packages to interrogate large and diverse data.
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- Bioinformatics: Including but not limited to: GWAS, QTL, bulk/scRNA-seq & epigenomics, machine learning, high-performance computing, GitHub, GitHub Actions, Docker/Singularity containers, DockerHub, conda, Nextflow, reproducibility.
- R: Created 36 R packages to date, including on Bioconductor and CRAN. Experienced in created Shiny Apps and Rmarkdown reports.
- Python: Regularly uses ML packages (e.g. sklearn, tensorflow, Keras). Developed and own IP for PubReporter, a software for extracting and conducting topic modelling/NLP on relevant scientific literature at scale.
- Javascript/HTML/CSS: Created 6+ websites, web apps, and interactive reports. Developed templates to automatically render websites on-the-fly from CSVs using Javascript.
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Communication
Effective and engaging scientific presentations to a variety of audiences.
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- Peers: Extensive experience presenting research proposals/findings to both internal and external labs/conferences. Invited speaker at leading research institutions. Diverse, multi-disciplinary and global collaborative network.
- Students: Teaching assistant and/or guest lecturer for courses in diverse fields (biological anthropology, neuroscience, computational biology).
- Public: Developed and delivered numerous community engagement programs for a wide variety of stakeholders, including students (preschool through postgraduate), community members, and patients (e.g. Children’s National Hospital, Parkinson’s UK).
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Project Management
Coordinates multiple independent projects at once with researchers of varying degrees of education and research experience. Effective handling of many projects at once.
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- Documentation: Detailed and understandable in-code documentation is second-nature.
- Version control: Extensive and daily use of git, GitHub Issues, GitHub Projects.
- Supervision: Supervises numerous student research projects.
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Publications
Artificial intelligence for neurodegenerative experimental models
Alzheimer’s & Dementia (2023) http://doi.org/10.1002/alz.13479
N/A
2023
SJ Marzi, BM Schilder, A Nott, C Sala Frigerio, S Willaime-Morawek, M Bucholc, DP Hanger,C James, PA Lewis, I Lourida, W Noble, F Rodriguez-Algarra, JA Sharif, M Tsalenchuk, LM Winchester, U Yaman, Z Yao, DEMON Network, JM Ranson, DJ Llewellyn
Artificial intelligence for dementia genetics and omics
Alzheimer’s & Dementia (2023) http://doi.org/10.1002/alz.13427
N/A
2023
C Bettencourt, NG Skene, S Bandres-Ciga, E Anderson, LM Winchester, IF Foote, J Schwartzentruber, JA Botia, M Nalls, A Singleton, BM Schilder, J Humphrey, SJ Marzi, CE Toomey, A Al Kleifat, EL Harshfield, V Garfield, C Sandor, S Keat, S Tamburin, C Sala Frigerio, I Lourida, DEMON Network, JM Ranson, DJ Llewellyn
Artificial intelligence for dementia research methods optimization
Alzheimer’s & Dementia (2023) http://doi.org/10.1002/alz.13441
N/A
2023
M Bucholc, C James, A Al Khleifat, A Badhwar, N Clarke, A Dehsarvi, CR Madan, SJ Marzi, C Shand, BM Schilder, S Tamburin, HM Tantiangco, I Lourida, DJ Llewellyn, JM Ranson
EpiCompare: R package for the comparison and quality control of epigenomic peak files
Bioinformatics Advances (2023) 13(1):vbad049; https://doi.org/10.1093/bioadv/vbad049
N/A
2023
S Choi, BM Schilder, L Abbasova, AE Murphy, NG Skene
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies
Nature Genetics (2022) https://doi.org/10.1038/s41588-021-00976-y
N/A
2022
K de Paiva Lopes, G JL Snijders, J Humphrey, A Allan, M Sneeboer, E Navarro, BM Schilder…T Raj
News
- Microglial transcriptomics meets genetics: new disease leads (Nature Reviews Neurology, 2022)
- Mighty MiGA: Microglial Genomic Atlas Zeros in on Causal AD Risk Variants (ALZFORUM, 2022)
- Can a Human Microglial Atlas Guide Brain Disorder Research? (Mount Sinai Health System, 2022)
- Polygenic Scores Paint Microglia as Culprits in Alzheimer’s (ALZFORUM, 2021)
Multi-omic insights into Parkinson’s Disease: From genetic associations to functional mechanisms
Neurobiology of Disease (2021) 105580; https://doi.org/10.1016/j.nbd.2021.105580
N/A
2021
BM Schilder, E Navarro, T Raj
Fine-Mapping of Parkinson’s Disease Susceptibility Loci Identifies Putative Causal Variants
Human Molecular Genetics (2021) ddab294; https://doi.org/10.1093/hmg/ddab294
N/A
2021
BM Schilder, T Raj
echolocatoR: An Automated End-to-End Statistical and Functional Genomic Fine-Mapping Pipeline
Bioinformatics (2021) btab658; https://doi.org/10.1093/bioinformatics/btab658
N/A
2021
BM Schilder, J Humphrey, T Raj
MungeSumstats: A Bioconductor Package for the Standardisation and Quality Control of Many GWAS Summary Statistics
Bioinformatics (2021) 37(23):4593-4596; https://doi.org/10.1093/bioinformatics/btab665
N/A
2021
A Murphy, BM Schilder, NG Skene
Dysregulation of mitochondrial and proteo-lysosomal genes in Parkinson’s disease myeloid cells
Nature Genetics (2021) https://doi.org/10.1101/2020.07.20.212407
N/A
2021
E Navarro, E Udine, K de Paiva Lopes, M Parks, G Riboldi, BM Schilder…T Raj
News
- Mount Sinai: Fighting Neurodegenerative Disorders (Mount Sinai Health System, 2019)
Phenome-wide and eQTL Associations of COVID-19 Genetic Risk Loci
iScience (2021) https://doi.org/10.1016/j.isci.2021.102550
N/A
2021
C Moon, BM Schilder, T Raj, K-l Huang
Genome-Wide Association Study of over 40,000 Bipolar Disorder Cases Provides Novel Biological Insights
Nature Genetics (2021) 53:817-829; https://doi.org/10.1038/s41588-021-00857-4
N/A
2021
N Mullins, AJ Forstner, KS O’Connell, B Coombes, JRI Coleman…BM Schilder… et al.
News
- Researchers identify 64 regions of the genome that increase risk for bipolar disorder (EurekAlert, 2021)
- Largest Bipolar Disorder Genetics Study Doubles Genetic Risk Factors (Nordic Society of Human Genetics and Precision Medicine, 2021)
Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs
PLOS Genetics (2020) 16(9):e1008549; https://doi.org/10.1101/499509
N/A
2020
S Ramdhani, E Navarro, E Udine, AG Efthymiou, BM Schilder, M Parks, A Goate, T Raj
Evolutionary shifts dramatically reorganized the human hippocampal complex
Journal of Comparative Neurology (2019) 528(17):3143-3170; https://doi.org/10.1002/cne.24822
N/A
2019
BM Schilder, HM Petry, PR Hof
FAIRshake: Toolkit to Evaluate the Findability, Accessibility, Interoperability, and Reusability of Research Digital Resources
Cell Systems (2019) 9; https://doi.org/10.1016/j.cels.2019.09.011
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2019
D Clarke, L Wang, A Jones, M Wojciechowicz, D Torre, K Jagodnik, S Jenkins, P McQuilton, Z Flamholz, M Silverstein, BM Schilder…A Ma’ayan
News
- Chosen as ‘Featured Frontmatter’ article in Cell Systems
Geneshot: search engine for ranking genes from arbitrary text queries
Nucleic Acids Research (2019) 47(W1):W571-W577; https://doi.org/10.1093/nar/gkz393
N/A
2019
A Lachmann, BM Schilder, ML Wojciechowicz, D Torre, MV Kuleshov, AB Keenan, A Ma’ayan
News
- Geneshot: Piercing the Literature to Identify and Predict Relevant Genes (University of Pittsburgh Health Sciences Library System Update, 2019)
- The Future of AI at the Hasso Plattner Institute for Digital Health at Mount Sinai (Mount Sinai Health System, 2020)
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks
Nucleic Acids Research (2018) 46(W1):W171-W179; https://doi.org/10.1093/nar/gky458
N/A
2018
DJB Clarke, MV Kuleshov, BM Schilder, D Torre, ME Duffy, AB Keenan, A Lachmann, AS Feldmann, GW Gundersen, MC Silverstein, Z Wang
News
- Mount Sinai Faculty Spotlight: Ma’ayan Lab (Mount Sinai Health System, 2018)
Defining elemental imitation mechanisms: A comparison of cognitive and motor-spatial imitation learning across object- and computer-based tasks
Journal of Cognition and Development (2015) 17(2):221-243; https://doi.org/10.1080/15248372.2015.1053483
N/A
2015
F Subiaul, L Zimmerman, E Renner, BM Schilder, R Barr
Take the monkey and run
Journal of Neuroscience Methods (2015) 248:28-31; http://doi.org/10.1016/j.jneumeth.2015.03.023
N/A
2015
KA Phillips, MK Hambright, K Hewes, BM Schilder, CN Ross, SD Tardif
News
- Monkeys on a Treadmill? A Conversation with Dr. Kimberley Phillips (Why Social Science?)
Working memory constraints on imitation and emulation
Journal of Experimental Child Psychology (2014) 128:190-200; http://doi.org/10.1016/j.jecp.2014.07.005
N/A
2014
F Subiaul, BM Schilder
Preprints
Identification of cell type-specific gene targets underlying thousands of rare diseases and subtraits
medRxiv (2023) https://doi.org/10.1101/2023.02.13.23285820
N/A
2023
KB Murphy, R Gordon-Smith, J Chapman, M Otani, BM Schilder, NG Skene
The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages
Research Square (2023) https://doi.org/10.21203/rs.3.rs-2399015/v1
N/A
2023
BM Schilder, AE Murphy, NG Skene
CUT&Tag recovers up to half of ENCODE ChIP-seq peaks
bioRxiv (2022) https://doi.org/10.1101/2022.03.30.486382
N/A
2022
D Hu, L Abbasova, BM Schilder, A Nott, NG Skene, SJ Marzi
Acknowledgements
eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs.
Nature Genetics (2021) 53:1290-1299; https://doi.org/10.1038/s41588-021-00924-w
N/A
2021
N Kerimov, JD Hayhurst, K Peikova et al.
Functionally-informed fine-mapping and polygenic localization of complex trait heritability
Nature Genetics (2020) https://doi.org/10.1038/s41588-020-00735-5
N/A
2020
O Weissbrod…AL Price
EEG oscillations reveal neural correlates of evidence accumulation
Frontiers in Decision Neuroscience (2012) 6(106):Jan-13; https://doi.org/10.3389/fnins.2012.00106
N/A
2012
M van Vugt, P Simen, L Nystrom, P Holmes, J Cohen
Trial-by-trial adaptation of decision making performance: a model-based EEG analysis
Interdisciplinary Perspectives on Cognition, Education, and the Brain (2011) 7; https://www.semanticscholar.org/paper/Trial-by-trial-adaptation-of-decision-making-a-EEG-Vugt-Simen/330371d08842ecd1bda332dd22351a7135b5cb1f
N/A
2011
M van Vugt, P Simen, J Cohen
Reviewerships
[Unpublished article]
Neuron (2023)
N/A
2023
[Unpublished article]
Bioinformatics (2022)
N/A
2022
CLIP: accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information
Bioinformatics (2021) https://doi.org/10.1093/bib/bbac502
N/A
2021
Z Peng, Z Li, Q Meng, B Zhao, L Kurgan
Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway
Neurobiology of Disease (2020) https://doi.org/10.3389/fimmu.2021.639613
N/A
2020
O Uriarte Huarte, D Kyriakis, T Heurtaux, Y Pires-Afonso, K Grzyb, R Halder, M Buttini, A Skupin, M Mittelbronn, A Michelucci
Deconstructing cerebellar development cell by cell
PLOS Genetics (2019) https://doi.org/10.1371/journal.pgen.1008630
N/A
2019
MJ van Essen, S Nayler, EBE Becker, J Jacob
[Unpublished article]
Nature Neuroscience (2019)
N/A
2019
Invited Talks
Decomposing the phenome: learning the latent genomic structure underlying thousands of diseases and traits
Neuroepidemiology of Aging Webinar
RUSH Alzheimer’s Disease Center (RADC)
RUSH University
N/A
2022
Drug (re)discovery in the age of genomics: multi-omic strategies for identifying disease treatments
Department Seminar
3D (Drug, Disease, Delivery) Center / Department of Pharmaceutical Sciences
University of South Dakota
N/A
2022
Statistical and functional genetic fine-mapping across multiple disease
Seminar
Alzheimer’s Disease Sequencing Project
Columbia University / Icahn School of Medicine at Mount Sinai
N/A
2020
Statistical and functional genetic fine-mapping across multiple disease
Laboratory of Neurogenetics Friday Workshop
National Institute on Aging
National Institutes of Health
N/A
2020
Conference Talks
rworkflows: taming the Wild West of R packages
EuroBioc2023
Bioconductor
N/A
2023
rworkflows: taming the Wild West of R packages
BioC2023
Bioconductor
N/A
2023
Systematic quantification of animal model viability across human diseases
Informatics-Synapse Joint Early Career Researcher Meeting
UK Dementia Research Institute (UK DRI)
N/A
2022
Automated genetic fine-mapping of neurological disorders
London Genetics Network
The Genetics Society
N/A
2020
Parkinson’s disease derived monocytes show alteration in the phago-lysosomal pathway
American Society of Human Genetics (ASHG) Annual Meeting
American Society of Human Genetics (ASHG)
N/A
2019
Co-contributor
Marmoset Social
Society for Neuroscience (SfN)
N/A
2016
JB Johnston Club for Evolutionary Neuroscience
Society for Neuroscience (SfN)
N/A
2016
JB Johnston Club for Evolutionary Neuroscience
Society for Neuroscience (SfN)
N/A
2014
Conference Posters
Identification of cell type-specific gene targets underlying thousands of rare diseases and clinical phenotypes
Genomics of Rare Diseases (2023) https://coursesandconferences.wellcomeconnectingscience.org/event/genomics-of-rare-disease-20230424/
N/A
2023
BM Schilder, KB Murphy, R Gordon-Smith, J Chapman, M Otani, NG Skene
Statistical and Functional Fine-Mapping as a Powerful Tool to Unravel the Biological Etiology of Bipolar Disorder
Biological Psychiatry (2023) 93(9):S18; https://doi.org/10.1016/j.biopsych.2023.02.063
N/A
2023
M Koromina, A Ravi, BM Schilder, B Muller, J Coleman, T Raj
Systematic quantification of animal model viability across human disease
UK Dementia Research Institute Scientific Advisory Board (2023)
N/A
2023
BM Schilder, NG Skene
Systematic quantification of animal model viability across human disease
Rising Scientist Day at Imperial College London (2022)
N/A
2022
BM Schilder, NG Skene
A compehensive statistical and functional fine-mapping pipeline applied to Bipolar Disorder GWAS risk loci
European Neuropsychopharmacology (2022) 63:e14; http://dx.doi.org/10.1016/j.euroneuro.2022.07.037
N/A
2022
M Koromina, A Ravi, BM Schilder, B Muller, J Coleman, T Raj, N Mullins
Genetic Effects on Human Microglia Transcriptome in Neuropsychiatric Diseases
Biological Psychiatry (2021) 89(9):S84-S85; https://doi.org/10.1016/j.biopsych.2021.02.225
N/A
2021
G Snijders, K de Paiva Lopes, J Humphrey, S Allan, M Sneeboer, R Navarro, BM Schilder, R Vialle, M Parks, R Missall, W van Zuiden, F Gigase, R Kubler, AB van Berlekom, C Bottcher, J Priller, R Kahn, L de Witte, T Raj
Cell-type-specific reconstruction of primate evolution from genomic positive selection
Rising Scientist Day at Imperial College London (2020)
N/A
2020
K Murphy, BM Schilder, NG Skene
Automated genetic and functional fine-mapping of Parkinson’s Disease Loci.
American Society of Human Genetics (2019)
N/A
2019
BM Schilder, T Raj
Parkinson’s disease derived monocytes show alteration in the phago-lysosomal pathway
American Society of Human Genetics (2019)
N/A
2019
E Udine, E Navarro, …BM Schilder, …T Raj
Learning X2K: Parameter Optimization via Genetic Algorithms to Calibrate the Expression2Kinases Pipeline
Illuminating the Druggable Genome (2018)
N/A
2018
BM Schilder, A Lachmann, M Kuleshov, A Ma’ayan
Learning X2K: Parameter Optimization via Genetic Algorithms to Calibrate the Expression2Kinases Pipeline
Big Data 2 Knowledge - Library of Integrated Network-Based Cellular Signatures (LINCS) (2018)
N/A
2018
BM Schilder, A Lachmann, M Kuleshov, A Ma’ayan
The evolution of the human hippocampus and neuroplasticity
Association for American Physical Anthropologists (2017) https://www.abstractsonline.com/pp8/index.html#!/4071/presentation/4471
N/A
2017
BM Schilder, BJ Bradley, CC Sherwood
The molecular evolution of plasticity and the human hippocampus
Society for Neuroscience (2016) https://www.abstractsonline.com/pp8/index.html#!/4071/presentation/4471
N/A
2016
BM Schilder, BJ Bradley, CC Sherwood
Effects of exercise on disease progression and cognition in the marmoset EAE model
JB Johnston Club for Evolutionary Neuroscience (2015)
N/A
2015
KA Phillips, MK Hambright, K Hewes, BM Schilder, B Jagessar, B t’Hart, SD Tardif
The effects of climatic trends, variability, and rates of change on mammalian brain evolution
Association for American Physical Anthropologists (2015)
N/A
2015
BM Schilder, WA Barr, R Bobe, CC Sherwood
Individual, Observational, and Imitation Learning in Orangutans and Children
Association for American Physical Anthropologists (2015)
N/A
2015
E Renner, BM Schilder, F Subiaul
The helper hinderer task revisited: an infant eye tracking study
The George Washington University Research Day (2014)
N/A
2014
A Gokhale, BM Schilder, F Subiaul
Dendritic morphology of pyramidal neurons across the visual stream: A direct comparison of chimpanzees and humans
Society for Neuroscience (2013)
N/A
2013
BM Schilder, O Adeyo
The striatum in the evolution of learned vocalizations: Understanding the neurobiological precursors to human speech using a chimpanzee model
Society for Neuroscience (2013)
N/A
2013
S Bianchi, T Duka, G Muntane, BM Schilder, CD Stimpson, WD Hopkins
Imitation & emulation in a novel box task
Association for Psychological Science (2013)
N/A
2013
L Zimmerman, N Brito, C Mendelson, R Barr, E Renner, BM Schilder, F Subiaul
A study of imitation and working memory in 2- to 4- year-olds
Association for Psychological Science (2013)
N/A
2013
R Barr, F Subiaul, L Zimmerman, L Renner, BM Schilder, C Mendelson, L Golojuch
The impact of wealth on sharing preferences in children
Child Development Society (2013)
N/A
2013
J Miller, BM Schilder, L Peizer, F Subiaul
Research Experience
Lead Data Scientist
120/80 MKTG
- - 2019
- Offered data-driven consultation services to a wide portfolio of high-profile digital healthcare, pharmaceutical and biotech companies.
- Developed a suite of propietary softwares to extract customised business intelligence from the published literature. Generated customised and interpetable reports to clients.
- Provided clients guidance on strategic data analysis, publication and transparency.
Bioinformatician II
Icahn School of Medicine at Mount Sinai (Department of Neuroscience / Department of Neurology / Department of Genetics & Genomics / Ronald M. Loeb Center for Alzheimer’s Disease)
2020 - 2018
- Developed machine learning systems to integrate large-scale multi-omics datasets (e.g. whole-genome sequencing, bulk and single-cell RNA-seq, epigenomics, clinical data) to uncover the molecular mechanisms underlying neurodegenerative diseases (e.g. Alzheimer’s, Parkinson’s, ALS).
- Computationally identified specific disease-causal variants, pathways and cell-types for subsequent functional wet lab validation (e.g. CRISPR-cas9 editing in patient-derived cell cultures, iPSCs and cerebral organoids).
Bioinformatician II
Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)
2018 - 2017
- Conducted computational systems biology research. Integrated and analyzed large-scale genomic and biomedical data (e.g. Python, R, JavaScript).
- Developed evolutionary algorithm to optimize gene network kinase regulator prediction (eXpression2Kinases).
- Developed and deployed computational tools, software, databases and web applications for basic and clinical research, resulting in 3 peer-reviewed publications.
Participant
Technische Universität Dresden / eMed (Summer School in Systems Medicine)
2017
- Attended lectures and extended skills in extraction and analysis of big data from biomedical and neurogenomic resources.
- Developed, performed and wrote manuscript for collaborative bioinformatics research project in less than one week.
Participant
Icahn School of Medicine at Mount Sinai (Scientific Computing & Data Science)
2016
- Intensive summer school in high-performance computing, coding, genome database utilization and bioinformatics methods including transcriptomics and genetic association testing.
Collaborator
Trinity University / Southwestern National Primate Research Center (Department of Neuroscience)
2017 - 2014
- Investigated the neurobiological mechanisms underlying the ameliorating effects of exercise on relapse-remitting Multiple Sclerosis.
Teaching Assistant / Project Leader
The George Washington University / Rutgers University (Department of Anthropology)
2014
- Served as Teaching Assistant while excavating Lower Paleolithic hominin sites (Homo, Paranthropus).
- As Project Leader, investigated the running biomechanics of local Daasanach tribespeople while mentoring undergraduate students.
Research Assistant
The George Washington University (Department of Anthropology)
2013 - 2011
- Performed dissection, histology, microscopy and quantitative stereology in post-mortem primate brain tissues.
- Trained junior and senior personnel on lab protocols.
Senior Lab Manager
The George Washington University (Department of Speech, Language & Hearing Sciences)
2013 - 2011
- Organized and trained dozens of undergraduates to conduct weekly cognitive development research; designed and/or directly contributed to over 15 research projects in two years.
Volunteer Researcher
University of Winnipeg / University of Belgrade (Department of Anthropology / Department of Archaeology)
2012
- Excavated Paleolithic fossils and tools (H. heidelbergensis, H. neanderthalensis) at Mala Balanica, Velika Balanica, and Pešturina sites.
Volunteer Researcher
Universidad de Murcia (Department of Zoology & Physical Anthropology)
2011
- Excavated Paleolithic fossils and tools from Cueva Negra (H. heidelbergensis) and Sima de las Palomas (H. neanderthalensis) with an international research team.
Volunteer Research Intern
American Museum of Natural History (Division of Anthropology)
2011
- Contributed to paleoanthropological research on primate fossils using 3D morphometry imaging equipment including Minolta, Microscribe and CT.
Paid Research Intern
Princeton University (Princeton Neuroscience Institute)
2010
- Investigated the neural basis of decision-making in humans.
- Recruited participants, recorded EEG and analyzed data in MATLAB.
Student Researcher
Brown University (Department of Cognitive, Linguistic & Psychological Sciences)
2010 - 2009
- Experimental Analysis of Animal Behavior & Cognition: Conducted various operant conditioning experiments on rats. Gained experience in animal behavioral training, data collection, and data analysis in MATLAB.
- Laboratory in Genes and Behavior: Tested transgenic mice with modified N-type voltage-gated calcium channel subunits in a battery of cognitive and sensorimotor tasks. Results were published.
Teaching / Mentoring Experience
Research Mentor
Imperial College London (Department of Brain Sciences / Department of Life Sciences)
- - 2020
- Mentored students and affiliated projects:
- Kitty Murphy (PhD): ‘Evolutionary pressures on cell types: leveraging species differences to gain insight into neurodegenerative disease risk’
- Sheen Lei (BSc): ‘Benchmarking cell-type-specific enrichment of genome-wide disease signatures’
- Ted Reese (MSc): ‘Computational cell-type annotation of single-cell epigenomics data’
- Xindong Sun (MSc): ‘Benchmark of Targeted insertion of promoters sequencing (TIP-seq) on histone modification H3K27ac and H3K27me3 in K562 cell line’
- Shuhan Shen (MSc): ‘Evaluation and optimisation of methods for identifying the cell types underlying genetic disease signatures’
- Lusheng Li (MSc): ‘Genetic identification of cell types underlying mammalian phenotypes’
- Sera Choi (BSc): ‘EpiCompare: R package for QC and benchmarking epigenetic datasets’
- Emilie Cottard (MSc) & Will Lunt (BSc): ‘A meta-analysis of selective cell-type vulnerability in Parkinson’s Disease neuropathology’
- Jai Chapman (BSc): ‘Expression Weighted Cell Type Enrichment as a Tool for Identifying Cell Types Underlying Rare Disease Phenotypes’
- Bobby Gordon-Smith (MSc): ‘Identification of cell types involved in rare disease-associated human phenotypes’
- Leyla Abbasova (MSc): ‘Analysis and optimisation of CUT&Tag for epigenomic profiling of the brain’
- Barney Hill (BSc): ‘Identification of cell-types associated with latent factors inferred from phenome-wide GWAS summary statistics’
Research Mentor
Icahn School of Medicine at Mount Sinai (Department of Neuroscience / Department of Neurology / Department of Genetics & Genomics / Ronald M. Loeb Center for Alzheimer’s Disease)
2020 - 2019
- Mentored MS, MD, and PhD students in projects focused on computational exploration of phenotype clustering and genomic regulation of neurodegenerative diseases.
Research Co-mentor
Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)
2018
- Mentored students and affiliated projects:
- Vivian Utti (BSc): ‘ChEA3: Transcription Factor Enrichment Analysis’ as part of the Summer Research Training Program in Biomedical Big Data Science.
- Mary Duffy (PhD): ‘Predicting upstream kinase regulators from interaction network databases’
- Zach Flamholz (BSc): ‘modEnrichr: a suite of gene set enrichment analysis tools for model organisms’
Guest Lecturer
Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)
2018
- Lectured on data visualization in Python and Jupyter notebooks in the PhD/MD course ‘Programming for Big Data Biomedicine’.
Research Mentor
The George Washington University (Department of Anthropology)
2017 - 2016
- Mentored students and affiliated projects:
- Jamie Kleiner (BSc): ‘Animal model simulating MS and exercise’s impact on adult hippocampal neurogenesis’
Teaching Assistant
The George Washington University (Department of Anthropology)
2015
- Course: ‘Human Brain Evolution’
- Guest lectured, graded all assignments and exams, and provided additional educational support during office hours.
Teaching Assistant
The George Washington University (Department of Psychology)
2014
- Course: ‘Biological Psychology’
- Led undergraduates in article discussions, graded all assignments and exams, and provided additional educational support during office hours.
Teaching Assistant
The George Washington University (Department of Anthropology)
2014 - 2013
- Course: ‘Biological Anthropology’
- Led undergraduate students in two, 2-hour lab sessions per week, graded lab assignments and exams, and provided additional educational support during office hours.
Research Mentor
The George Washington University (Department of Psychology)
2013 - 2012
- Mentored students and affiliated projects:
- Anushka Gokhale (BSc): ‘Infants’ Social Assessment of Characters Through Eye Gaze’
Lab Protocol Trainer
The George Washington University (Department of Anthropology)
2013 - 2011
- Trained undergraduate, graduate, and post-doctoral researchers in Social Cognition Lab and Lab for Evolutionary Neuroscience in a variety of methodological research protocols.
Software Packages
anndataR 
Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyze your single-cell data.
https://github.com/scverse/anndataR
N/A
1.
gptPhD
Query Large Language Models for the purposes of systematically extracting biomedical knowledge.
https://github.com/neurogenomics/gptPhD
N/A
2.
ThreeWayTest
Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants
https://github.com/bschilder/ThreeWayTest
N/A
3.
SCAVENGE
Variant to function mapping at single-cell resolution through network propagation
https://github.com/sankaranlab/SCAVENGE
https://doi.org/10.1038/s41587-022-01341-y
N/A
4.
rworkflows
Continuous integration for R packages. Automates testing, documentation website building, and containerised deployment
https://github.com/neurogenomics/rworkflows
https://doi.org/10.21203/rs.3.rs-2399015/v1
N/A
5.
TIPseeker
R package for post-processing [single-cell] TIP-seq data
https://github.com/neurogenomics/TIPseeker
N/A
6.
PeakyFinders
R package for mining, calling, and importing epigenomic peaks
https://github.com/neurogenomics/PeakyFinders
N/A
7.
graphiti
Extract colour palettes from graffiti artworks.
https://github.com/bschilder/graphiti
N/A
8.
SkillNet
Creates user-specific contribution networks from GitHub Organization repositories
https://github.com/neurogenomics/SkillNet
N/A
9.
phenoRx
Make cell type-specific predictions for patients based on clinical phenotypes and/or risk genes.
https://github.com/neurogenomics/phenomix
N/A
10.
phenomix
R package for the exploration and analysis of many genotype-phenotype datasets at once
https://github.com/neurogenomics/phenomix
N/A
11.
MAGMA_Celltyping
Identify cell types underlying the associations found in GWAS summary statistics
https://github.com/neurogenomics/MAGMA_Celltyping
N/A
12.
EpiCompare
R package for QC and benchmarking epigenetic datasets
https://github.com/neurogenomics/EpiCompare
https://doi.org/10.1101/2022.07.22.501149
N/A
14.
MultiEWCE
R package for analysing multiple gene lists using EWCE
https://github.com/neurogenomics/MultiEWCE
https://doi.org/10.1101/2023.02.13.23285820
N/A
15.
HPOExplorer
Functions for working with the Human Phenotype Ontology data
https://github.com/neurogenomics/HPOExplorer
https://doi.org/10.1101/2023.02.13.23285820
N/A
16.
MungeSumstats
Standardise the format of summary statistics from GWAS
https://github.com/neurogenomics/MungeSumstats
https://doi.org/10.1093/bioinformatics/btab665
N/A
18.
scNLP
Tools for applying natural language processing (NLP) techniques to single-cell (sc) omics data
https://github.com/neurogenomics/scNLP
N/A
19.
scKirby
Automated ingestion and conversion of various single-cell data formats
https://github.com/neurogenomics/scKirby
N/A
20.
geneshotR
R package for querying and processing results from Geneshot.
https://github.com/bschilder/geneshotR
N/A
21.
templateR
Self-updating template for developing R packages
https://github.com/neurogenomics/templateR
https://doi.org/10.21203/rs.3.rs-2399015/v1
N/A
22.
echoverseTemplate
Self-updating template for creating echoverse R packages.
https://github.com/RajLabMSSM/echoverseTemplate/
https://doi.org/10.1093/bioinformatics/btab658
N/A
23.
echolocatoR
R package for end-to-end statistical and functional fine-mapping with extensive dataset access
https://github.com/RajLabMSSM/echolocatoR
https://doi.org/10.1093/bioinformatics/btab658
N/A
24.
echodata
Examples of fine-mapped GWAS summary statistics, data formatting functions, and API access to the echolocatoR Fine-mapping Portal
https://github.com/RajLabMSSM/echodata
https://doi.org/10.1093/bioinformatics/btab658
N/A
25.
echoannot
Functions for annotating genomic data with annotations and epigenomic data
https://github.com/RajLabMSSM/echoannot
https://doi.org/10.1093/bioinformatics/btab658
N/A
26.
echoplot
R package for LocusZoom-inspired GWAS/QTL visualization, with API access to LD panels
https://github.com/RajLabMSSM/echoplot
https://doi.org/10.1093/bioinformatics/btab658
N/A
27.
echoconda
Various utility functions to find, build, and use conda environments from within R
https://github.com/RajLabMSSM/echoconda
https://doi.org/10.1093/bioinformatics/btab658
N/A
28.
echotabix
Tabix indexing and querying
https://github.com/RajLabMSSM/echotabix
https://doi.org/10.1093/bioinformatics/btab658
N/A
29.
echoLD
LD downloading and processing.
https://github.com/RajLabMSSM/echoLD
https://doi.org/10.1093/bioinformatics/btab658
N/A
30.
echofinemap
Statistical and functional fine-mapping functions.
https://github.com/RajLabMSSM/echofinemap
https://doi.org/10.1093/bioinformatics/btab658
N/A
31.
echodeps
Creates interactive dependency networks for R packages
https://github.com/RajLabMSSM/echodeps
https://doi.org/10.1093/bioinformatics/btab658
N/A
32.
echogithub
Access and process metadata from GitHub
https://github.com/RajLabMSSM/echogithub
https://doi.org/10.1093/bioinformatics/btab658
N/A
33.
devoptera
Practical tools for R developers
https://github.com/RajLabMSSM/devoptera
https://doi.org/10.1093/bioinformatics/btab658
N/A
34.
downloadR
Single- and multi-threaded downloading functions
https://github.com/RajLabMSSM/downloadR
https://doi.org/10.1093/bioinformatics/btab658
N/A
35.
catalogueR
R package for rapid API-access and colocalization of summary statistics from eQTL Catalogue
https://github.com/RajLabMSSM/catalogueR
https://doi.org/10.1093/bioinformatics/btab658
N/A
36.
TopicModeler
Proprietary Python package to run advanced topic modeling on text corpuses.
N/A
37.
JobReporter
Proprietary Python package to extract job postings and company employee listings and generate interactive business intelligence reports.
N/A
38.
PubReporter
Proprietary Python package for extract relevant scientific literature, gather citations, and generate interactive business intelligence reports.
N/A
39.
Databases / Web Apps
EpiArchives
Public archive for EpiCompare reports.
https://github.com/neurogenomics/EpiArchives
https://doi.org/10.1101/2022.07.22.501149
N/A
1.
Rare Disease Celltyping Portal
Web portal connecting to multiple R Shiny apps to explore, visualize, and download cell type-specific enrichment results and systematically prioritised gene targets for over 6,000 rare disease phenotypes.
https://github.com/neurogenomics/rare_disease_celltyping_apps
https://neurogenomics.github.io/rare_disease_celltyping_apps/home
https://doi.org/10.1101/2023.02.13.23285820
N/A
2.
Parkinson’s Disease Omics Review
Data and code associated with the Parkinson’s Disease review paper by Schilder, Navarro & Raj (Neurobiology of Disease, 2021)
https://github.com/RajLabMSSM/PD_omics_review
https://rajlabmssm.github.io/PD_omics_review/
https://doi.org/10.1016/j.nbd.2021.105580
N/A
3.
Selective Vulnerability Meta-analysis
Selective Vulnerability Meta-analysis: Shiny app dedicated to the exploration and dissemination of meta-analysed cell counts manually curated and harmonised from the Parkinson’s Disease literature
https://github.com/neurogenomics/SelectiveVulnerabilityMetaAnalysis
N/A
4.
MAGMA Files Public
Gene enrichment files for hundreds of GWAS generated with Multi-marker Analysis of GenoMic Annotation (MAGMA) for use in downstream analyses
https://github.com/neurogenomics/MAGMA_Files_Public
N/A
5.
echolocatoR Fine-mapping Portal
Access to interactive plots and fine-mapping results across many GWAS/QTL datasets using echolocatoR
https://github.com/RajLabMSSM/Fine_Mapping_Shiny
https://rajlab.shinyapps.io/Fine_Mapping_Shiny
https://doi.org/10.1093/bioinformatics/btab658
N/A
6.
COVID-19 Patient Tracker
Web app for summarizing and visualizing real-time EHR data of COVID-19 patients within the Mount Sinai Health System
N/A
7.
Tensor Decomposition Shiny App
Interactive application to explore and download all results and plots from Ramdhani et al. (PLOS Genetics, 2020)
https://github.com/RajLabMSSM/Tensor_myeloid
https://rajlab.shinyapps.io/Tensor_myeloid
https://doi.org/10.1101/499509
N/A
8.
Hippocampal Evolution
Interactive code, results and visualization for the manuscript “Evolutionary selective pressures dramatically expanded and reorganized the human hippocampal complex”
https://github.com/bschilder/Hippo_Eco
https://bschilder.github.io/Hippo_Eco/HPsubfield_eco
https://doi.org/10.1002/cne.24822
N/A
9.
Geneshot 
Flexible tool to identify genes associated with any biomedical term and to predict novel target genes
http://amp.pharm.mssm.edu/geneshot
https://doi.org/10.1093/nar/gkz393
N/A
10.
X2K
eXpression 2 Kinases (X2K) Web: Automated computational pipeline to infer kinase regulators from weighted or unweighted gene lists
http://amp.pharm.mssm.edu/X2K
https://doi.org/10.1093/nar/gky458
N/A
11.
Websites
Personal Website
https://github.com/bschilder/BMSchilder
https://bschilder.github.io/BMSchilder
N/A
1.
Grants
Total (all grants): $2,949,872
Total (as primary applicant): $311,382
N/A
N/A
N/A
EuroBioc2023 Scholarship,
Bioconductor
Project: ‘rworkflows: taming the Wild West of R packages’
N/A
2023
News
- Awarded to support attending the EuroBioc2023 meeting.
- Role: Primary applicant
- PI: BM Schilder
- Amount: $250
BioC2023 Scholarship,
Bioconductor
Project: ‘rworkflows: taming the Wild West of R packages’
N/A
2023
News
- Awarded to support attending the BioC2023 meeting. Additionally included free lodging.
- Role: Primary applicant
- PI: BM Schilder
- Amount: $1500
Junior Scientist Conference Grant,
The Genetics Society
Project: ‘Identification of cell type-specific gene targets underlying thousands of rare diseases and subtraits’
N/A
2023
- Role: Primary applicant
- PI: BM Schilder
- Amount: £750
Imperial UK Research Institute Impact Acceleration Account,
Imperial College London
Project: ‘Creating commercial kit solutions for single cell epigenetic profiling of histone marks and transcription factors’
N/A
2023
- Role: Co-applicant
- PI: NG Skene
- Amount: £80,000
Turing Community Award,
Alan Turing Institute
Project: ‘Multi-omic medicine: dissecting the cell-type-specific molecular mechanisms underlying neurodegenerative disease genomics’
N/A
2024 - 2022
- Role: Primary applicant
- PI: BM Schilder
- Amount: £1,500
National Institutes of Health
Project: ‘Statistical and functional fine-mapping of bipolar disorder genetic risk loci’
N/A
2022
- Role: Co-applicant
- PI: N Mullins
Collaborative Single Cell and Spatial Transcriptomics Studies Award Programme,
UK Dementia Research Institute
Project: ‘Amplifying genome coverage of single cell epigenetic profiling of the human brain’
N/A
2021
- Role: Co-applicant
- PI: D Hu, NG Skene
- Amount: £12,790
National Institutes of Health
Project: “Cognitive Systems Analysis of Alzheimer’s Disease Genetic and Phenotypic Data”
N/A
2020
- Role: Co-applicant
- PI: T Raj, D Knowles
- Amount: $2,523,431
UK Dementia Research Institute
Project: ‘UK DRI at Imperial Distinguished Studentship’
N/A
2024 - 2020
- Role: Primary applicant
- PI: BM Schilder
- Amount: £217,000
The Michael J. Fox Foundation
Project: “The Role of Peripheral Myeloid Cells in Parkinson’s Disease”
N/A
2019 - 2017
- Role: Fundee
- PI: T Raj
The Michael J. Fox Foundation
Project: ‘Functional Fine-Mapping of LRRK2 Locus’
N/A
2020 - 2017
- Role: Fundee
- PI: T Raj
National Science Foundation
Project: ‘The evolution of the hippocampus and adult neurogenesis: novel insights into the origins of human memory’
N/A
2017
- Role: Primary applicant
- PI: BM Schilder
- Amount: $31 543
Wenner-Gren
Project: ‘The evolution of the hippocampus and adult neurogenesis: insights into the origins of human memory’
N/A
2017
- Role: Primary applicant
- PI: BM Schilder
- Amount: $19,512
Leakey Foundation
Project: ‘The evolution of the hippocampus and adult neurogenesis: Novel insights into the origins of human memory’
N/A
2016
- Role: Primary applicant
- PI: BM Schilder
- Amount: $15,000
COSMOS Club
Project: ‘The evolution of adult neurogenesis across primates’
N/A
2016
- Role: Primary applicant
- PI: BM Schilder
- Amount: $3,250
Awards
Prize for Computational Reproducibility in Dementia Research,
UK Dementia Research Institute
Project: ‘MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics’
N/A
2022
News
- Awarded honourable mention
Poster Competition,
Rising Scientist Day
Project: ‘Systematic quantification of animal model viability across human diseases’
N/A
2022
News
- Awarded prize for research poster competition.
Award for Outstanding Contribution,
NEUROHACK, Deep Dementia Phenotyping Network (DEMON)
Project: ‘Predicting ALS drug targets using integrative multi-modal deep learning’
N/A
2022
News
- Individually awarded for outstanding contributions during the NEUROHACK 2022, a competitive 4-day hackathon to apply AI in finding ALS therapeutic solutions.
Prize for Computational Reproducibility in Dementia Research,
UK Dementia Research Institute
Project: ‘echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline’
N/A
2021
Centre Photography Competition,
UK Dementia Research Institute
Project: ‘Wildfire Circle, Golden Brain, Wildfire, Geneshot, Geology of Biology, Neon Brain’
N/A
2021
Art of the Brain,
Friedman Brain Institute, Icahn School of Medicine
Project: ‘Wildfire’
N/A
2019
News
- Awarded 2nd place and Featured on the cover of Biological Psychiatry: Volume 87, Issue 12 (2020). Exhibited and auctioned at the Grady Alexis Gallery (New York City), where all proceeds were voluntarily donated to the Diversity in Neuroscience Initiative.
Affiliations
- Synapse Working Group
- Informatics Working Group
N/A
- Genetics & Omics Working Group
- Experimental Models Working Group
- Drug Discovery & Trials Optimisation Working Group
N/A
- Bipolar Disorder Working Group
N/A
- Bioconductor Cloud Methods Working Group
- Active developer
N/A
Data Visualisation / Artwork Portfolio
echoverse Dependency Graph
N/A
2022
- Interactve graph showing the dependency structure of all packages within the echoverse suite.
3D Human Phenotype Ontology
N/A
2023
- 3D force-directed graph of the Human Phenotype Ontology (clouds above) with kernel density estimation projected from the x/y planes (mountains below). Connections represent the hierarchical relationships between rare diseases and their associated symptoms/phenotypes.
- Associated preprint
Multi-scale Rare Disease Mechanisms
N/A
2023
- Network of systematically prioritised gene therapy targets for rare diseases
- Associated preprint
Curriculum Vitae Connexa
N/A
2023
- Term co-occurrence network generated by analysing all data that went into this CV.
Lights in the dark genome: the current state of Parkinson’s research
N/A
2021
- The majority of PD genetics research has focused on a relatively small number of genes. Above, are the top 75 most commonly mentioned genes in the PD literature, extracted using Geneshot.
- Associated study
Circos
N/A
2020
- Colocalised genetic loci across a variety of neurological disease GWAS and cell-type-specific QTLs.
- Associated study
Wildfire Circle
N/A
2019
- Awarded 2nd place in the 2019 Art of the Brain competition, put on by the Mount Sinai’s Friedman Brain Institute.
- Exhibited and auctioned at the Grady Alexis Gallery (New York City), where all proceeds were donated to the Diversity in Neuroscience Initiative .
- Featured on cover of Biological Psychiatry.
Wildfire
N/A
2019
- Transcriptomic data from 16k+ individual brain cells (shown as points) after reducing the dimensionality with an autoencoder and UMAP. 5 million tracts are shown interconnecting these cells, where shorter tract length represents greater similarity in their molecular profiles.
Extracurricular Experience
Competitive Running Career
- 8+ years of varsity and Division I cross country, winter track, and spring track throughout high school and college.
- Year-round, daily training and travel to weekly competitions necessitated a dedicated and regimented lifestyle in order to succeed as a student-athlete
- Running remains a passion of mine and I enjoy training for ultra-marathons in my free time.
- This passion, work ethic and self-insight have carried over to all aspects of my life, including my career as a researcher.
.
- - 2003
Music Production
- Writes, records, produces and performs original music.
- Instruments: keys, percussion, vocals, etc.
- Proficient in Logic Pro X Digital Audio Workstation (DAW).
- Experiments with generative AI.
.
- - 1995